Solution (source code)

= Solution

Treat the reacting <carbon> skeletons as an activated glycosyl donor and a 3-substituted <indole>. The new linkage is \b[an anomeric-carbon–indole-C2 <carbon>–<carbon> bond], not a bond to <indole> <nitrogen>. A plausible purely chemical pathway is a dissociative <electrophilic aromatic substitution>:

* Activation of the anomeric diphosphate <leaving group>, for example by acid, permits cleavage of its bond to the <anomeric carbon>. The ring <oxygen> stabilizes the resulting <glycosyloxocarbenium ion>, represented by the resonance pair $\mathrm{O_{ring}-C_1^+\leftrightarrow O_{ring}^+=C_1}$. A nearby diphosphate counterion may remain in a <contact ion pair>.
* The <indole> C2–C3 <pi bond> attacks C1 through C2. This makes the new C1–C2 bond and gives an <arenium ion>, with C2 temporarily tetrahedral and still bearing its original hydrogen. Positive charge can be delocalized over the pyrrolic portion, including an indolium resonance contributor.
* A base removes that C2 hydrogen. The C2–H bond <electrons> restore the C2–C3 <pi bond> and <aromaticity>, releasing the <C-glycosylation> product while retaining N–H.

The drawn donor and product have opposite anomeric faces: the anomeric <leaving group> is on the same face as the hydroxymethyl <substituent>, while the new <carbon> <substituent> is on the opposite face. Thus the target has \b[net inversion at the <anomeric carbon>]. A tight <ion pair> with the departing group shielding its original face can rationalize opposite-face capture in this proposed pathway. A freely solvated planar <oxocarbenium ion> would not by itself guarantee exclusive inversion; competing faces, <hydrolysis> and other products remain possible without an experimentally specified chemical promoter. This is a plausible non-enzymatic mechanism, not a claim that the uncatalysed reaction is rapid or clean in neutral water.

\Image[/past-exam-of-the-chemistry-b-course-of-the-university-of-cambridge/2021/paper-2-glycosylation-mechanism.png]
{title=Original non-enzymatic C–C bond-forming mechanism with explicit reactive atoms}